- mothurOut("The chimera.seqs command reads a fastafile and creates a sorted priority score list of potentially chimeric sequences (ideally, the sequences should already be aligned).\n");
- mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors and method. fasta is required.\n");
- mothurOut("The filter parameter allows you to specify if you would like to apply a 50% soft filter. The default is false. \n");
- mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs. The default is true. \n");
- mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
- mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is pintail. \n");
- mothurOut("The chimera.seqs command should be in the following format: \n");
- mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
- mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, processors=2, method=yourMethod) \n");
- mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+
+ //"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name"
+ //m->mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n");
+ m->mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n");
+ m->mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters, search, realign.\n");
+ m->mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n");
+ m->mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
+ m->mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n");
+ m->mothurOut("The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n");
+ m->mothurOut("The method parameter allows you to specify the method for finding chimeric sequences. The default is pintail. Options include bellerophon, ccode and chimeracheck \n");
+ m->mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
+ m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras. \n");
+ m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences.\n");
+ m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences. \n");
+ m->mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
+ m->mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences.\n");
+ m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with.\n");
+ m->mothurOut("The ksize parameter allows you to input kmersize. \n");
+ m->mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n");
+ m->mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
+ m->mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
+ m->mothurOut("The minsim parameter allows you .... \n");
+ m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
+ m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
+ m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+ m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. -used only by chimeraslayer. \n");
+ m->mothurOut("The realign parameter allows you to realign the query to the potential paretns. Choices are true or false, default false. -used only by chimeraslayer. \n");
+ m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
+ m->mothurOut("Details for each method: \n");
+ m->mothurOut("\tpintail: \n");
+ m->mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=300, increment=25, conservation=not required, but will improve speed, quantile=not required, but will greatly improve speed. \n");
+ m->mothurOut("\t\tIf you have run chimera.seqs using pintail a .quan and .freq file will be created for your template, if you have not provided them for use in future command executions.\n");
+ m->mothurOut("\tbellerophon: \n");
+ m->mothurOut("\t\tparameters: fasta=required, filter=F, processors=1, window=1/4 length of seq, increment=25, correction=T. \n");
+ m->mothurOut("\tccode: \n");
+ m->mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n");
+ m->mothurOut("\tchimeracheck: \n");
+ m->mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n");
+ m->mothurOut("\tchimeraslayer: \n");
+ m->mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n");
+ m->mothurOut("The chimera.seqs command should be in the following format: \n");
+ m->mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
+ m->mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");